Sun 23 Dec 22:22:49 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2oh1-1.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oh1-1.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oh1-1.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:00 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh1-1.5-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 803 and 0 Target number of residues in the AU: 803 Target solvent content: 0.4606 Checking the provided sequence file Detected sequence length: 179 Maximum limit of NCS related copies: 16 Number of NCS-related molecules: 4 Adjusted target number of residues: 716 Adjusted target solvent content: 0.52 Input MTZ file: 2oh1-1.5-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 65.646 99.855 122.905 90.000 90.000 90.000 Input sequence file: 2oh1-1.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 5728 target number of atoms Had to go as low as 0.50 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 77.501 1.460 Wilson plot Bfac: 16.22 127339 reflections ( 90.67 % complete ) and 0 restraints for refining 6362 atoms. Observations/parameters ratio is 5.00 ------------------------------------------------------ Starting model: R = 0.3251 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2641 (Rfree = 0.000) for 6362 atoms. Found 510 (534 requested) and removed 277 (267 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.67 1.63 Round 1: 630 peptides, 27 chains. Longest chain 69 peptides. Score 0.894 Round 2: 654 peptides, 12 chains. Longest chain 118 peptides. Score 0.937 Round 3: 660 peptides, 11 chains. Longest chain 136 peptides. Score 0.941 Round 4: 665 peptides, 12 chains. Longest chain 172 peptides. Score 0.940 Round 5: 663 peptides, 12 chains. Longest chain 122 peptides. Score 0.940 Taking the results from Round 3 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 6452 restraints for refining 6321 atoms. 1070 conditional restraints added. Observations/parameters ratio is 5.04 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2756 (Rfree = 0.000) for 6321 atoms. Found 278 (531 requested) and removed 108 (265 requested) atoms. Cycle 2: After refmac, R = 0.2581 (Rfree = 0.000) for 6488 atoms. Found 203 (545 requested) and removed 26 (272 requested) atoms. Cycle 3: After refmac, R = 0.2337 (Rfree = 0.000) for 6655 atoms. Found 203 (559 requested) and removed 38 (279 requested) atoms. Cycle 4: After refmac, R = 0.2225 (Rfree = 0.000) for 6792 atoms. Found 165 (572 requested) and removed 31 (286 requested) atoms. Cycle 5: After refmac, R = 0.2135 (Rfree = 0.000) for 6910 atoms. Found 171 (581 requested) and removed 25 (290 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.64 1.60 Round 1: 666 peptides, 8 chains. Longest chain 172 peptides. Score 0.948 Round 2: 669 peptides, 7 chains. Longest chain 170 peptides. Score 0.951 Round 3: 666 peptides, 10 chains. Longest chain 166 peptides. Score 0.945 Round 4: 671 peptides, 8 chains. Longest chain 172 peptides. Score 0.950 Round 5: 669 peptides, 9 chains. Longest chain 172 peptides. Score 0.947 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 6566 restraints for refining 6741 atoms. 1081 conditional restraints added. Observations/parameters ratio is 4.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2264 (Rfree = 0.000) for 6741 atoms. Found 255 (566 requested) and removed 96 (283 requested) atoms. Cycle 7: After refmac, R = 0.2173 (Rfree = 0.000) for 6885 atoms. Found 183 (579 requested) and removed 34 (289 requested) atoms. Cycle 8: After refmac, R = 0.2097 (Rfree = 0.000) for 7017 atoms. Found 183 (590 requested) and removed 28 (295 requested) atoms. Cycle 9: After refmac, R = 0.2044 (Rfree = 0.000) for 7152 atoms. Found 190 (602 requested) and removed 36 (301 requested) atoms. Cycle 10: After refmac, R = 0.2007 (Rfree = 0.000) for 7280 atoms. Found 179 (613 requested) and removed 55 (306 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.63 1.59 Round 1: 668 peptides, 9 chains. Longest chain 172 peptides. Score 0.947 Round 2: 673 peptides, 7 chains. Longest chain 172 peptides. Score 0.952 Round 3: 671 peptides, 9 chains. Longest chain 172 peptides. Score 0.948 Round 4: 672 peptides, 8 chains. Longest chain 172 peptides. Score 0.950 Round 5: 671 peptides, 12 chains. Longest chain 134 peptides. Score 0.942 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 6687 restraints for refining 6948 atoms. 1169 conditional restraints added. Observations/parameters ratio is 4.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2176 (Rfree = 0.000) for 6948 atoms. Found 313 (583 requested) and removed 104 (291 requested) atoms. Cycle 12: After refmac, R = 0.2119 (Rfree = 0.000) for 7141 atoms. Found 207 (601 requested) and removed 38 (300 requested) atoms. Cycle 13: After refmac, R = 0.2052 (Rfree = 0.000) for 7300 atoms. Found 173 (614 requested) and removed 47 (307 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2014 (Rfree = 0.000) for 7407 atoms. Found 166 (623 requested) and removed 63 (311 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1978 (Rfree = 0.000) for 7495 atoms. Found 186 (630 requested) and removed 70 (315 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.63 1.59 Round 1: 669 peptides, 8 chains. Longest chain 172 peptides. Score 0.949 Round 2: 672 peptides, 7 chains. Longest chain 172 peptides. Score 0.952 Round 3: 667 peptides, 8 chains. Longest chain 172 peptides. Score 0.949 Round 4: 669 peptides, 10 chains. Longest chain 152 peptides. Score 0.945 Round 5: 661 peptides, 13 chains. Longest chain 134 peptides. Score 0.937 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 6929 restraints for refining 7078 atoms. 1424 conditional restraints added. Observations/parameters ratio is 4.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2159 (Rfree = 0.000) for 7078 atoms. Found 305 (594 requested) and removed 87 (297 requested) atoms. Cycle 17: After refmac, R = 0.2101 (Rfree = 0.000) for 7275 atoms. Found 179 (612 requested) and removed 58 (306 requested) atoms. Cycle 18: After refmac, R = 0.2033 (Rfree = 0.000) for 7382 atoms. Found 166 (621 requested) and removed 40 (310 requested) atoms. Cycle 19: After refmac, R = 0.1978 (Rfree = 0.000) for 7484 atoms. Found 162 (630 requested) and removed 51 (315 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1945 (Rfree = 0.000) for 7576 atoms. Found 180 (637 requested) and removed 62 (318 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.63 1.59 Round 1: 666 peptides, 10 chains. Longest chain 166 peptides. Score 0.945 Round 2: 673 peptides, 6 chains. Longest chain 172 peptides. Score 0.954 Round 3: 672 peptides, 7 chains. Longest chain 172 peptides. Score 0.952 Round 4: 671 peptides, 9 chains. Longest chain 172 peptides. Score 0.948 Round 5: 666 peptides, 11 chains. Longest chain 134 peptides. Score 0.943 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 7012 restraints for refining 7134 atoms. 1489 conditional restraints added. Observations/parameters ratio is 4.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2153 (Rfree = 0.000) for 7134 atoms. Found 349 (599 requested) and removed 92 (299 requested) atoms. Cycle 22: After refmac, R = 0.2093 (Rfree = 0.000) for 7374 atoms. Found 188 (620 requested) and removed 43 (310 requested) atoms. Cycle 23: After refmac, R = 0.2040 (Rfree = 0.000) for 7496 atoms. Found 156 (631 requested) and removed 43 (315 requested) atoms. Cycle 24: After refmac, R = 0.1977 (Rfree = 0.000) for 7596 atoms. Found 152 (639 requested) and removed 42 (319 requested) atoms. Cycle 25: After refmac, R = 0.1945 (Rfree = 0.000) for 7680 atoms. Found 173 (647 requested) and removed 53 (323 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.63 1.59 Round 1: 668 peptides, 8 chains. Longest chain 172 peptides. Score 0.949 Round 2: 669 peptides, 9 chains. Longest chain 162 peptides. Score 0.947 Round 3: 671 peptides, 8 chains. Longest chain 172 peptides. Score 0.950 Round 4: 670 peptides, 9 chains. Longest chain 171 peptides. Score 0.947 Round 5: 668 peptides, 10 chains. Longest chain 135 peptides. Score 0.945 Taking the results from Round 3 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 7045 restraints for refining 7207 atoms. 1557 conditional restraints added. Observations/parameters ratio is 4.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2155 (Rfree = 0.000) for 7207 atoms. Found 330 (605 requested) and removed 92 (302 requested) atoms. Cycle 27: After refmac, R = 0.2092 (Rfree = 0.000) for 7424 atoms. Found 224 (625 requested) and removed 35 (312 requested) atoms. Cycle 28: After refmac, R = 0.2043 (Rfree = 0.000) for 7588 atoms. Found 151 (639 requested) and removed 51 (319 requested) atoms. Cycle 29: After refmac, R = 0.1980 (Rfree = 0.000) for 7671 atoms. Found 165 (645 requested) and removed 47 (322 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1956 (Rfree = 0.000) for 7775 atoms. Found 159 (654 requested) and removed 75 (327 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.63 1.59 Round 1: 665 peptides, 11 chains. Longest chain 156 peptides. Score 0.942 Round 2: 668 peptides, 9 chains. Longest chain 171 peptides. Score 0.947 Round 3: 665 peptides, 12 chains. Longest chain 156 peptides. Score 0.940 Round 4: 666 peptides, 9 chains. Longest chain 166 peptides. Score 0.946 Round 5: 662 peptides, 10 chains. Longest chain 166 peptides. Score 0.943 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 7159 restraints for refining 7237 atoms. 1698 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2156 (Rfree = 0.000) for 7237 atoms. Found 348 (607 requested) and removed 106 (303 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2110 (Rfree = 0.000) for 7456 atoms. Found 196 (628 requested) and removed 69 (314 requested) atoms. Cycle 33: After refmac, R = 0.2036 (Rfree = 0.000) for 7563 atoms. Found 180 (636 requested) and removed 44 (318 requested) atoms. Cycle 34: After refmac, R = 0.1989 (Rfree = 0.000) for 7683 atoms. Found 156 (646 requested) and removed 62 (323 requested) atoms. Cycle 35: After refmac, R = 0.1961 (Rfree = 0.000) for 7753 atoms. Found 186 (653 requested) and removed 69 (326 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.63 1.59 Round 1: 670 peptides, 9 chains. Longest chain 172 peptides. Score 0.947 Round 2: 671 peptides, 11 chains. Longest chain 162 peptides. Score 0.944 Round 3: 668 peptides, 10 chains. Longest chain 166 peptides. Score 0.945 Round 4: 666 peptides, 13 chains. Longest chain 135 peptides. Score 0.939 Round 5: 663 peptides, 15 chains. Longest chain 128 peptides. Score 0.934 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 7210 restraints for refining 7257 atoms. 1726 conditional restraints added. Observations/parameters ratio is 4.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2175 (Rfree = 0.000) for 7257 atoms. Found 347 (609 requested) and removed 102 (304 requested) atoms. Cycle 37: After refmac, R = 0.2113 (Rfree = 0.000) for 7482 atoms. Found 203 (630 requested) and removed 55 (315 requested) atoms. Cycle 38: After refmac, R = 0.2056 (Rfree = 0.000) for 7603 atoms. Found 176 (640 requested) and removed 45 (320 requested) atoms. Cycle 39: After refmac, R = 0.2011 (Rfree = 0.000) for 7717 atoms. Found 162 (649 requested) and removed 69 (324 requested) atoms. Cycle 40: After refmac, R = 0.1984 (Rfree = 0.000) for 7786 atoms. Found 180 (656 requested) and removed 58 (328 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.63 1.59 Round 1: 668 peptides, 10 chains. Longest chain 166 peptides. Score 0.945 Round 2: 671 peptides, 11 chains. Longest chain 172 peptides. Score 0.944 Round 3: 671 peptides, 11 chains. Longest chain 171 peptides. Score 0.944 Round 4: 675 peptides, 8 chains. Longest chain 172 peptides. Score 0.950 Round 5: 663 peptides, 15 chains. Longest chain 128 peptides. Score 0.934 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 127339 reflections ( 90.67 % complete ) and 7121 restraints for refining 7234 atoms. 1589 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2151 (Rfree = 0.000) for 7234 atoms. Found 362 (607 requested) and removed 96 (303 requested) atoms. Cycle 42: After refmac, R = 0.2104 (Rfree = 0.000) for 7484 atoms. Found 217 (630 requested) and removed 66 (315 requested) atoms. Cycle 43: After refmac, R = 0.2055 (Rfree = 0.000) for 7614 atoms. Found 168 (641 requested) and removed 47 (320 requested) atoms. Cycle 44: After refmac, R = 0.2007 (Rfree = 0.000) for 7715 atoms. Found 155 (649 requested) and removed 48 (324 requested) atoms. Cycle 45: After refmac, R = 0.1968 (Rfree = 0.000) for 7802 atoms. Found 142 (657 requested) and removed 58 (328 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.63 1.59 Round 1: 670 peptides, 10 chains. Longest chain 162 peptides. Score 0.946 Round 2: 672 peptides, 8 chains. Longest chain 171 peptides. Score 0.950 Round 3: 667 peptides, 12 chains. Longest chain 165 peptides. Score 0.941 Round 4: 671 peptides, 9 chains. Longest chain 171 peptides. Score 0.948 Round 5: 666 peptides, 13 chains. Longest chain 162 peptides. Score 0.939 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2oh1-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 127339 reflections ( 90.67 % complete ) and 7220 restraints for refining 7268 atoms. 1713 conditional restraints added. Observations/parameters ratio is 4.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2164 (Rfree = 0.000) for 7268 atoms. Found 0 (610 requested) and removed 15 (305 requested) atoms. Cycle 47: After refmac, R = 0.2064 (Rfree = 0.000) for 7231 atoms. Found 0 (597 requested) and removed 0 (304 requested) atoms. Cycle 48: After refmac, R = 0.2002 (Rfree = 0.000) for 7218 atoms. Found 0 (595 requested) and removed 0 (303 requested) atoms. Cycle 49: After refmac, R = 0.1961 (Rfree = 0.000) for 7213 atoms. TimeTaking 97.32